There has been talk of Cena being the leader of Nexus, but that would be the dumbest twist ever. I mean, you can't have Nexus brutally attacking Cena week after week and leaving him out cold JUST to fool the audience.
First of all, what would the point of that be? Is it really worth Cena getting beat up just so he can surprise everyone a few months later?
Second of all, why would they keep attacking their leader and costing him valuable wins? Why not someone else?
Thirdly, Nexus are supposed to be rebels, standing up against the WWE and it makes sense for them to target the face of the company. It wouldn't make any sense for them to attack him if they secretly knew he was behind them.
Obviously, inconsistency and implausibility is typical of WWE writing (just look at Daniel Bryan's sudden and unexplained change) but no writer with any self-worth would do something like this.